The p53 tumor suppressor is central to human DNA repair, damage checkpoints and many aspects of human biology. Importantly, most cancers are altered for p53 function. There is considerable variation in p53 dependent expression across >400 targeted genes leading to differences in p53-mediated biological consequences, due in part to variation in target response element (RE) sequence. We found that RE motifs differ considerably from the in vitro derived RE consensus target sequence previously described as 2 copies of RRRCWWGYYY separated by a spacer of up to 13 bases. We have focused on RE functionality, i.e., the ability of REs to support transactivation by p53. To directly assess functionality of human REs, i.e., transactivation responsiveness, we developed promoter systems in budding yeast for variable human p53 expression and have translated many of the findings to human cells in culture and ex vivo. That led us to the identification of super-transactivating sequences (STARES) that provide high transactivation at low p53 levels. Remarkably, we observed that transactivation specificity is conserved among p53 family proteins. We found that p53 can transactivate through noncanonical binding sequences including half-sites, greatly expanding the p53 regulatory network. We extended these studies genome-wide using ChIP-Seq analysis to identify p53 binding sites and associated gene expression changes following p53 activation in cancer cells as well as in primary T-lymphocytes after treatment with anti-cancer drugs. Similar to cancer cells, we found that most p53 bound sites contained a canonical p53 response element (2 tandem RRRCWWGYYY decamers without spacer). Importantly, we showed that p53 can also engage transcription using half-sites across the genome and we went on to define the minimal binding unit for p53-mediated transcription as a 1/2-site. Among differentially expressed genes associated with p53 binding several are relevant to immunity and inflammation Moreover, in a global approach we are determining the p53 network by examining p53 binding across the genome, induced gene expression and protein interactors using mass spectrometry methods, under diverse stress conditions. We identified 45 novel p53 protein interactors in response to the commonly-used chemotherapeutic drug Doxorubicin. Remarkably, we found in our ChIPseq studies that p53 bound the transcriptional regulatory regions of 97% of these interactors, revealing potential regulatory p53 loops and thereby provide a novel systems biology approach to understanding the p53 stress responsive network. CANCER-ASSOCIATED p53 MUTANTS. With inclusion of immune response-related TLR genes into the p53 network, we evaluated the effect of 25 tumor-associated p53 mutants on TLR gene family expression after transient transfection in p53-null cancer cell. Changes in TLR transactivation patterns, including change-of-spectrum, were observed, suggesting that p53 tumor status might be an important factor in adjuvant therapy employing TLR pathways to treat cancer. Furthermore, we demonstrated that tumor-associated p53 mutants that induced expression of TLR3, enhanced cytokine and chemokine responses mediated by this receptor after exposing cells to TLR3 ligand poly-I:C alone or in presence of Doxorubicin. We also found that functional rescue of loss-of-function p53 mutants by the p53 reactivating drug RITA, restored TLR gene expression in a mutant p53 cell line and also enhanced DNA damage induced-apoptosis via TLR3 signaling. We propose that chemotherapeutic manipulation of normal or mutantp53 responses along with immune challenges that include TLRs could enhance inflammatory/immune type responses to environmental factors. Furthermore, several p53 mutants also altered the expression of the innate immune related APOBEC3 (A3) gene family. In particular, overexpression of a group of tumor-associated p53 mutants in p53 null cancer cells actually promoted expression of A3B, which normally is repressed by WT p53, suggesting a clear gain of function phenotype for these p53 mutants. Since TP53 gene mutations occur in many human cancers, it is important to identify anticancer drugs that specifically target p53 mutant tumor cells. We are pursuing the identification of synthetic lethal (SL) genes with genome-wide siRNA-based screens, that when reduced in expression in p53 mutant cells cause death or reduced growth. The SLs are expected to lead to potential targets and provide opportunities for anticancer drug development. We have identified several SL targets for two of the most frequent tumor-associated p53 mutants (R175H and R273H) in the presence of anticancer drug etoposide. We currently are validating several of these SL genes. p53 NETWORK EVOLUTION. We are investigating evolution of REs in terms of responsiveness to p53. Individual REs exhibited marked differences in potential transactivation as well as widespread turnover of functional REs during p53 network evolution. Among validated p53 REs conserved between rodents and humans, one third were comprised of 1/2- or 3/4-sites, each with a perfect consensus-site suggesting a selective advantage in retaining weak p53 REs. Similar to those observations, we identified in our recent ChIPseq cancer cell study that 60% of the p53 REs were conserved at the sequence level in rodents. Using Gene Ontology (GO) for gene function classification to identify those potential p53 target genes associated with DNA metabolism and repair functionswe found that only a few of the p53 RE sequences were conserved in rodents in agreement with our earlier findings. Around 120 potential human target genes associated with DNA metabolism were found to be bound by p53. Most of them can also interact directly with p53 protein. We are using nanostring technology to validate the expression of the corresponding genes under stressed and unstressed conditions. THE INFLUENCE OF p53 ON HUMAN IMMUNE RESPONSES. We have established that p53 plays important physiologic roles in the immune system. p53 upregulates most members of TLR family in human primary and cancer cells to consequently enhance TLR-dependent production of proinflammatory cytokines in response to cognate ligands. We also found that p53 can collaborate with NFkappaB to strongly alter several immune/inflammatory responses in primary lymphocytes and macrophages from healthy volunteers,. Transcriptome analysis identified global p53/NF-kappaB cooperation on expression of immune response genes, including chemokines and interleukins. Accordingly, we generated a p53 ChIP-seq dataset associated with global gene expression from primary human lymphocytes under non-stress conditions as well as after ex-vivo treatment with well-known p53 activators (Doxorubicin and Nutlin). Around 200 genes that exhibited a p53/ligand synergistic response to chemotherapeutic agents have been identified Included were genes related to immune/inflammation processes, several of which have been validated as p53 potential targets using qRT-PCR and Nanostring technologies. Among these genes we found several of the human cytidine deaminase A3 gene family involved in the innate immune that deal with retrotransposons and RNA virus infection are also subject to p53 transcriptional control. Moreover we observed that Respiratory syncytial virus (RSV), the of major cause of respiratory problems in young children worldwide, induced p53 protein activation, resulting in the expression of several A3 genes in a p53-dependent manner and influencing negatively the virus replication. These observations together with discovery of other immune related p53 target genes provide new insights into the relationship between p53, environmental stress and immunity, and they suggest approaches for cancer.
| Alessandrini, Federica; Pezzè, Laura; Menendez, Daniel et al. (2018) ETV7-Mediated DNAJC15 Repression Leads to Doxorubicin Resistance in Breast Cancer Cells. Neoplasia 20:857-870 |
| Nguyen, Thuy-Ai T; Grimm, Sara A; Bushel, Pierre R et al. (2018) Revealing a human p53 universe. Nucleic Acids Res : |
| Aparicio-Cuevas, Manuel A; Rivero-Cruz, Isabel; Sánchez-Castellanos, Mariano et al. (2017) Dioxomorpholines and Derivatives from a Marine-Facultative Aspergillus Species. J Nat Prod 80:2311-2318 |
| Lowe, Julie M; Nguyen, Thuy-Ai; Grimm, Sara A et al. (2017) The novel p53 target TNFAIP8 variant 2 is increased in cancer and offsets p53-dependent tumor suppression. Cell Death Differ 24:181-191 |
| Menendez, Daniel; Nguyen, Thuy-Ai; Snipe, Joyce et al. (2017) The Cytidine Deaminase APOBEC3 Family Is Subject to Transcriptional Regulation by p53. Mol Cancer Res 15:735-743 |
| Currier, Jenna M; Cheng, Wan-Yun; Menendez, Daniel et al. (2016) Developing a Gene Biomarker at the Tipping Point of Adaptive and Adverse Responses in Human Bronchial Epithelial Cells. PLoS One 11:e0155875 |
| Menendez, Daniel; Lowe, Julie M; Snipe, Joyce et al. (2016) Ligand dependent restoration of human TLR3 signaling and death in p53 mutant cells. Oncotarget 7:61630-61642 |
| Shatz, Maria; Shats, Igor; Menendez, Daniel et al. (2015) p53 amplifies Toll-like receptor 5 response in human primary and cancer cells through interaction with multiple signal transduction pathways. Oncotarget 6:16963-80 |
| Sharma, Vasundhara; Jordan, Jennifer J; Ciribilli, Yari et al. (2015) Quantitative Analysis of NF-?B Transactivation Specificity Using a Yeast-Based Functional Assay. PLoS One 10:e0130170 |
| Nguyen, Thuy-Ai; Menendez, Daniel; Resnick, Michael A et al. (2014) Mutant TP53 posttranslational modifications: challenges and opportunities. Hum Mutat 35:738-55 |
Showing the most recent 10 out of 32 publications
